ExpHunterSuite
This is the development version of ExpHunterSuite; for the stable release version, see ExpHunterSuite.
Package For The Comprehensive Analysis Of Transcriptomic Data
Bioconductor version: Development (3.21)
The ExpHunterSuite implements a comprehensive protocol for the analysis of transcriptional data using established *R* packages and combining their results. It covers all key steps in DEG detection, CEG detection and functional analysis for RNA-seq data. It has been implemented as an R package containing functions that can be run interactively. In addition, it also contains scripts that wrap the functions and can be run directly from the command line.
Author: James Perkins [aut, cre] 
, Pedro Seoane Zonjic [aut] , Fernando Moreno Jabato [aut] , José Córdoba Caballero [aut] , Elena Rojano Rivera [aut] , Rocio Bautista Moreno [aut] , M. Gonzalo Claros [aut] , Isabel Gonzalez Gayte [aut], Juan Antonio García Ranea [aut]
Maintainer: James Perkins <jimrperkins at gmail.com>
citation("ExpHunterSuite")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("ExpHunterSuite")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ExpHunterSuite")| The Expression Hunter Suite | HTML | R Script |
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpressionWorkflow, Workflow |
| Version | 1.14.0 |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1.0) |
| Imports | ReactomePA, limma, edgeR, NOISeq, biomaRt, topGO, diffcoexp, DT, ggplot2, stringr, WGCNA, dplyr, AnnotationDbi, BiocGenerics, enrichplot, rmarkdown, stats, Biobase, DESeq2, ROCR, data.table, knitr, magrittr, SummarizedExperiment, miRBaseVersions.db, grDevices, graphics, utils, BiocParallel, MKinfer, matrixStats, ggupset, rlang, plyr, tidyr, GO.db, Matrix, fastcluster, DOSE, heatmaply, EnhancedVolcano, ggrepel, clusterProfiler, GenomicRanges, GenomicFeatures, tximport, annotatr, ggridges, FactoInvestigate, FactoMineR |
| System Requirements | |
| URL |
See More
| Suggests | optparse, PerformanceAnalytics, naivebayes, reshape2, org.Hs.eg.db, org.Mm.eg.db, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ExpHunterSuite_1.14.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/ExpHunterSuite |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ExpHunterSuite |
| Package Short Url | https://bioconductor.org/packages/ExpHunterSuite/ |
| Package Downloads Report | Download Stats |